# Trinotate error? See GTN Transcriptomics tutorials for alternatives! **URL:** \ **Category:** usegalaxy.eu support\ **Tags:** tool-deprecated, resources\ **Created:** [October 7, 2025, 1:31am UTC](https://help.galaxyproject.org/t/trinotate-error-see-gtn-transcriptomics-tutorials-for-alternatives/16353 "2025-10-07T01:31:23Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![igor](https://avatars.discourse-cdn.com/v4/letter/i/dec6dc/32.png) [@igor](https://help.galaxyproject.org/u/igor)\ **Post date:** [October 7, 2025, 1:31am UTC](https://help.galaxyproject.org/t/trinotate-error-see-gtn-transcriptomics-tutorials-for-alternatives/16353/1 "2025-10-07T01:31:23Z")
GDay, Trinotate jobs fail in Europe and Australia, with similar message: ```auto .import Trinotate.TaxonomyIndex TaxonomyIndex" | sqlite3 Trinotate.sqlite * Running CMD: wget "http://eggnogdb.embl.de/download/eggnog_4.5/data/NOG/NOG.annotations.tsv.gz" --2025-10-03 04:22:07-- http://eggnogdb.embl.de/download/eggnog_4.5/data/NOG/NOG.annotations.tsv.gz Resolving eggnogdb.embl.de... 194.94.44.170 Connecting to eggnogdb.embl.de|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 404 Not Found 2025-10-03 04:22:07 ERROR 404: Not Found. ``` [History](https://usegalaxy.eu/u/igor/h/trinotate). I see it for some time. Thank you! Igor ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [October 7, 2025, 4:53pm UTC](https://help.galaxyproject.org/t/trinotate-error-see-gtn-transcriptomics-tutorials-for-alternatives/16353/2 "2025-10-07T16:53:45Z")
Hi @igor I think this is expected. The source for the reference data is not available anymore due to the deprecated protocol. So, it ends up failing anywhere. I last looked at this in July → [Trinotate SQLite boilerplate unavailable on usegalaxy.eu?](https://help.galaxyproject.org/t/trinotate-sqlite-boilerplate-unavailable-on-usegalaxy-eu/15953). For history, the tool sort of worked at EU/AU long ago but never at ORG (persistent SQLite issues). Now it won’t work anywhere due to the missing reference data (which would be 10+ years outdated by now even if located!). We should probably get the tool tagged as deprecated on all the servers but there isn’t a good “meta” process for that (is a 1-off by admins, and can get stripped with the automatic tool updates). Maybe this will help to get it picked up → [Meta Request: Tag Trinotate as a deprecated tool at all UseGalaxy servers · Issue #430 · galaxyproject/usegalaxy-playbook · GitHub](https://github.com/galaxyproject/usegalaxy-playbook/issues/430). ---
**Author:** ![igor](https://avatars.discourse-cdn.com/v4/letter/i/dec6dc/32.png) [@igor](https://help.galaxyproject.org/u/igor)\ **Post date:** [October 8, 2025, 12:55am UTC](https://help.galaxyproject.org/t/trinotate-error-see-gtn-transcriptomics-tutorials-for-alternatives/16353/3 "2025-10-08T00:55:15Z")
Hi @jennaj It must be a recent change: I see completed Trinotate jobs in September, this year. I mean Galaxy Australia. Trinotate is used in a [tutorial](https://training.galaxyproject.org/topics/transcriptomics/tutorials/full-de-novo/tutorial.html) marked as Under development. What alternative(s) to Trinotate do you recommend? InterProScan, eggNOG Mapper, FGENESH, something else? Have a great day, Igor ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [October 8, 2025, 4:54pm UTC](https://help.galaxyproject.org/t/trinotate-error-see-gtn-transcriptomics-tutorials-for-alternatives/16353/4 "2025-10-08T16:54:40Z")
> [@igor](#): > > I see completed Trinotate jobs in September, this year. Oh! This is interesting. I wasn’t aware of the reference data being available, or with the current tool wrapper able to use it without running into that error. To solve this, I think asking the local administrators about how the configuration is different from the IUC wrapper/job container would be needed. This never worked at the ORG server, but the EU people might know more (I couldn’t get it to work there either, but maybe I tried it after the external tool was deprecated). Then for > [@igor](#): > > What alternative(s) to Trinotate do you recommend? InterProScan, eggNOG Mapper, FGENESH, something else? Those the ones I know about too. The GTN also includes **GOEnrichment** and **gProfiler GOSt** in their examples – but these would work after the transcripts are mapped to knowns, similar to how **annotateMyIDs** works. ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [April 8, 2026, 2:14am UTC](https://help.galaxyproject.org/t/trinotate-error-see-gtn-transcriptomics-tutorials-for-alternatives/16353/5 "2026-04-08T02:14:14Z")
The tool has been deprecated by the authors and is no longer available! For ideas about alternatives, try [Search results for 'trinotate' - Galaxy Community Help](https://help.galaxyproject.org/search?q=trinotate) or see our Transcriptomics tutorials 🎓 [Transcriptomics / Tutorial List](https://galaxyproject.github.io/training-material/topics/transcriptomics/). For adventurous hosting on **your own server** , please see [Trinotate SQLite boilerplate unavailable on usegalaxy.eu?](https://help.galaxyproject.org/t/trinotate-sqlite-boilerplate-unavailable-on-usegalaxy-eu/15953). ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [April 8, 2026, 2:15am UTC](https://help.galaxyproject.org/t/trinotate-error-see-gtn-transcriptomics-tutorials-for-alternatives/16353/6 "2026-04-08T02:15:10Z")